It is the first time a direct offspring of the two groups has ever been found.
"But we didn't even hope that we will be able to detect a direct descendant of these two groups", says Vivian Elephant, a researcher from the Institute of evolutionary anthropology of max Planck in Leipzig. "But I never thought we would be so lucky as to find an actual offspring of the two groups".
"It is striking that we find this Neanderthal/Denisovan child among the handful of ancient individuals whose genomes have been sequenced", said co-lead author Dr. Svante Pääbo, Director of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology. Some 90,000 years before William Shakespeare first brought the warring Capulets and Montagues to life, two hominins overcame what seems like an insurmountable obstacle-one was a Neanderthal, the other an entirely different species known as the Denisovan-to create a thriving interspecies family.
What we do know is that both Neanderthals and Denisovans disappeared around 40,000 years ago.
"They managed to catch it in the act - it's an awesome discovery", said Sharon Browning, a statistical geneticist at the University of Washington who was not involved in the new study. She began by hunting for a special set of genes found in the fuel-generating factories of the cell, called mitochondria.
The bone fragment shaking up the world of science was discovered there in 2012 and it has helped scientists understand that not only was interbreeding happening, it was happening a lot. If so, the story of Denisova's Neanderthal mother and Denisovan father may be less about star-crossed lovers than an unusual, albeit fairly common, hybrid coupling.
"Denisovans are so rare, so we don't know whether Denisovans and Neanderthals had an extensive overlap over long periods of time", he said.
That fragment came from an arm or leg bone - it is impossible to say which.
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The Denisovans were distinct but related to the Neanderthals.
The researchers sequenced the girl's genome from a 2.5-cm-wide bone fragment originally found in 2012 within the Denisova cave-the only place where evidence of Denisovans has been found-of the Altai Mountains in Russian Federation.
Indeed, the ancestors of modern-day Oceanians and Asians contain Denisovan DNA, while present-day non-Africans contain 2-4% Neanderthal DNA.
The sister groups are now understood to have diverged about 400,000 years ago, after their last common ancestor split with Homo sapiens at least 500,000 years ago. "Neandertals and Denisovans may not have had many opportunities to meet".
Denisova Cave is located on the far eastern edge of the Neanderthal's historic range.
Broader interbreeding may have gained momentum when modern humans emerged from Africa roughly 70,000 years ago.
During DNA sequencing of the bones discovered at the site, the researchers noticed that half of the chromosomes in Denisova 11 were similar to those of the other Denisovans and half of them were closer to those of the Neanderthals. Along with their colleagues, they carried out a genetic analysis of the piece of bone, finding that 40% of DNA fragments from the specimen matched Neanderthal DNA, while another 40% matched Denisovan DNA.
"Maybe Neanderthals and Denisovans were absorbed into the modern human populations", said Paabo.